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WPDB - PC-based Macromolecular Structure Interrogation
Version 1.0 Available
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WPDB (the Protein Data Bank through Microsoft Windows) is a macromolecular
structure query and analysis tool designed to complement rendering tools
such as Raswin and Kinemage.
Typical uses
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o Analysis of protein-protein and protein-ligand interactions
using the three-level zooming feature of the contact map
viewer and the residue selection feature of the 3D-viewer.
o Analysis of internal interactions in proteins to reveal
different folds (e.g. helix-helix hydrophobic stacking,
4-helix bundle) using contact map, hydrophobicity profile
and secondary structure selection feature in 3D-view.
o Analysis of sequence-structure correlations using sequence
search and static property profiles.
o Analysis of thermal motion using dynamic property profiles.
o Locate structures based on string searches of combinations
of PDB record types and/or sequence patterns.
To take a peek
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http://cuhhca.hhmi.columbia.edu/wpdb.html
How to get it?
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1. Anonymous ftp to cuhhca.hhmi.columbia.edu (128.59.98.1).
2. Change directory to /pub/programs/WPDB/doc.
3. Get the file install.
4. Follow instructions in the install file.
Note: Two compressed databases are available:
(i) random selection of 100 structures;
(ii) "unique" structures (320) as defined by Hobohm and Sander.
The README file in /pub/programs/WPDB/doc describes how to get the software
to build your own database.
Please send questions/comments/criticisms to wpdb at cuhhca.hhmi.columbia.edu
Some features
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o 20-fold compression of PDB files (minus REMARK records).
o Real-time query based on text string searches of PDB record
types and sequence.
o Clickable contact map with three levels of zooming for analyzing
intra- and inter-molecular interactions: level 1 - molecules,
level 2 - fragments, level 3 - atoms.
o Clickable profile with two levels of zooming to examine static
properties (volume, polarity, isoelectric point, hydrophobicity,
mean exposure) and isotropic temperature factor.
o 3D rendering tool with special capabilities for easy selection
of substructures and fragments by specifying chains,
secondary structure, residues (by location or name).
o Interoperability between display tools (3-D renderer, contact
maps and profile), i.e. selection made in one object will
be propagated to other visible display objects. For example
selecting a close contact in a contact map will be highlighted
in the structure.
o Secondary structure analysis according to Kabsch and Sander.
o Comprehensive manual and Windows-based help.
o A hook to the more advanced display features of Raswin.
Hardware/software requirements
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Intel 486/33 processor or above with a color monitor, 4MB RAM or better,
and Windows.
WPDB was designed, written and produced by Ilya Shindyalov and Phil Bourne.
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